News

2018-12-25

R-loopAtlas has been released !
(v1.0 -- First Open Version)

Now, the plant R-loop databese -- R-loopAtlas contains several function modules(such as Search Function, Browse Function, BLAST Function and so on) and related data of two model species (Arabidopsis thaliana and Oryza sativa Japonica).

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Welcome to R-loopAtlas, a database of R-loop.

R-loopAtlas is a specialized database for R-loop (RNA-DNA hybrid) which contains experimental R-loop data mainly via the ssDRIP-seq method. Users can get R-loop information from Arabidopsis thaliana genome or another species genome to investigate some questions that relevant to R-loop. For details, please go to other pages on the website.

Introduction

Based on experimental data.  In a general way, the data based on the experiment is more persuasive than the data based on a computational prediction. R-loopAtlas collecting mass R-loop data and the results save to backend server. These data about R-loops was identified by a biological experiment which mainly ssDRIP-seq, and including Arabidopsis thaliana,Oryza sativa and other species. Most of the previous methods for genome-wide R-loop detection had Minor defects, and ssDRIP-seq exhibits multiple advantages over the previous methods. That's why these data in R-loopAtlas have the advantage of high efficiency, low bias and strand specificity.

Genome-wide R-loop landscape.  We systematically analysed the genome-wide R-loop landscape in the model plant Arabidopsis thaliana by ssDRIP-seq analysis. The results demonstrated, similar to the R-loops from other organisms, Arabidopsis thaliana R-loops preferentially form in RNA Pol I, II and III-transcribed genes and some specific repetitive regions such as TEs, as well as centromere and telomere regions. The strong accumulation of antisense R-loops in the Arabidopsis genome differs greatly from the pattern in mammals. In mammals, high occupancy of R-loops in terminator regions is essential for proper transcriptional termination, but the level of R-loops in Arabidopsis gene terminators is low. More information please go to see article doi:10.1038/s41477-017-0004-x.

User's friendly platform.  R-loopAtlas offered a number of functions. We have added many serviceable tools, such as based JBrowse to visual exhibit customer's search results. Meanwhile, for search results, we offered the different format for download to meet various demands of research. Additionally, we band NCBI BLAST tool (BLAST+  executables) to R-loopAtlas for sequence alignment (genome library and R-loop library) by viroblast. See the website for additional features.

Raw Data

Inspired by the important roles of the special chromatin structure R-loops, here we report a new method, ssDRIP-seq, for genome-wide identification of R-loops.The sequencing data and processed files are available at Gene Expression Omnibus under accession number GSE95765 (Arabidopsis thaliana).